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Yorodumi- PDB-5n13: Second Bromodomain (BD2) from Candida albicans Bdf1 in the unboun... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5n13 | ||||||
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Title | Second Bromodomain (BD2) from Candida albicans Bdf1 in the unbound form | ||||||
Components | Bromodomain-containing factor 1 | ||||||
Keywords | TRANSCRIPTION / Bromodomain | ||||||
Function / homology | Function and homology information sporulation resulting in formation of a cellular spore / DNA repair / nucleus Similarity search - Function | ||||||
Biological species | Candida albicans (yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.2 Å | ||||||
Authors | Mietton, F. / Ferri, E. / Champlebouxm, M. / Zala, N. / Maubon, D. / Zhou, Y. / Harbut, M. / Spittler, D. / Garnaud, C. / Courcon, M. ...Mietton, F. / Ferri, E. / Champlebouxm, M. / Zala, N. / Maubon, D. / Zhou, Y. / Harbut, M. / Spittler, D. / Garnaud, C. / Courcon, M. / Chauvel, M. / d'Enfert, C. / Kashemirov, B.A. / Hull, M. / Cornet, M. / McKenna, C.E. / Govin, J. / Petosa, C. | ||||||
Funding support | France, 1items
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Citation | Journal: Nat Commun / Year: 2017 Title: Selective BET bromodomain inhibition as an antifungal therapeutic strategy. Authors: Mietton, F. / Ferri, E. / Champleboux, M. / Zala, N. / Maubon, D. / Zhou, Y. / Harbut, M. / Spittler, D. / Garnaud, C. / Courcon, M. / Chauvel, M. / d'Enfert, C. / Kashemirov, B.A. / Hull, M. ...Authors: Mietton, F. / Ferri, E. / Champleboux, M. / Zala, N. / Maubon, D. / Zhou, Y. / Harbut, M. / Spittler, D. / Garnaud, C. / Courcon, M. / Chauvel, M. / d'Enfert, C. / Kashemirov, B.A. / Hull, M. / Cornet, M. / McKenna, C.E. / Govin, J. / Petosa, C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5n13.cif.gz | 66.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5n13.ent.gz | 47.8 KB | Display | PDB format |
PDBx/mmJSON format | 5n13.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/n1/5n13 ftp://data.pdbj.org/pub/pdb/validation_reports/n1/5n13 | HTTPS FTP |
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-Related structure data
Related structure data | 5n15C 5n16C 5n17C 5n18C 2ouoS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 12626.337 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Candida albicans (yeast) / Gene: BDF1, CaO19.8593, CaO19.978 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5A4W8 | ||
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#2: Chemical | #3: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.49 Å3/Da / Density % sol: 50.62 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop Details: 0.1 M TRIS-HCl (pH 8.5) and 1 M ammonium phosphate. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9724 Å |
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Jul 26, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9724 Å / Relative weight: 1 |
Reflection | Resolution: 1.2→45.2 Å / Num. obs: 39415 / % possible obs: 97.9 % / Redundancy: 5.8 % / CC1/2: 0.999 / Rmerge(I) obs: 0.05 / Rpim(I) all: 0.022 / Net I/σ(I): 17 |
Reflection shell | Resolution: 1.2→1.24 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.263 / Mean I/σ(I) obs: 3 / Num. unique obs: 3330 / CC1/2: 0.918 / Rpim(I) all: 0.18 / % possible all: 83.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2OUO Resolution: 1.2→38.253 Å / SU ML: 0.08 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 14.31
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.2→38.253 Å
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Refine LS restraints |
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LS refinement shell |
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